ENST00000652958.1:n.1120T>C

Variant names:

• chr8-11578007-T-C
• rs10108511
• ENST00000652958.1:n.1120T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652958.1(LINC00208):​n.1120T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,892 control chromosomes in the GnomAD database, including 20,677 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.51 (20677 hom., cov: 31)
• Consequence: LINC00208 ENST00000652958.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.77
• Publications: 18 publications found

Genes affected

LINC00208 (HGNC:15535): (long intergenic non-protein coding RNA 208)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00208	NR_040035.1	n.784-363T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00208	ENST00000652958.1	n.1120T>C		non_coding_transcript_exon_variant	Exon 3 of 3
LINC00208	ENST00000653131.1	n.1190T>C		non_coding_transcript_exon_variant	Exon 2 of 2
LINC00208	ENST00000304233.3	n.1006-363T>C		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76774 AN: 151774 Hom.: 20671 Cov.: 31

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.0199

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.515

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.506 AC: 76819 AN: 151892 Hom.: 20677 Cov.: 31 AF XY: 0.490 AC XY: 36409 AN XY: 74232

African (AFR) AF: 0.603 AC: 24971 AN: 41400

American (AMR) AF: 0.402 AC: 6145 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2251 AN: 3468

East Asian (EAS) AF: 0.0197 AC: 102 AN: 5176

South Asian (SAS) AF: 0.324 AC: 1559 AN: 4810

European-Finnish (FIN) AF: 0.389 AC: 4112 AN: 10560

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36117 AN: 67896

Other (OTH) AF: 0.510 AC: 1072 AN: 2104

Alfa AF: 0.534 Hom.: 8946

Bravo AF: 0.506

Asia WGS AF: 0.210 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.15
DANN	Benign	0.42
PhyloP100		-2.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10108511; hg19: chr8-11435516;